1 LIN comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

1.1 LIN model characteristics

The main characteristics of the Test Case LIN (ling) CASAL model are:

  • one stock, ages 3 - 25
  • one area
  • years 1972 - 2018, projection years 2019 - 2023
  • two time steps: Dec_Aug and Sep_Nov
  • two stock categories: male and female
  • natural mortality-at-age is double exponential
  • sex-specific maturity ogives specified by age
  • sex-specific von Bertalanffy age-length relationship
  • sex-specific length-weight relationship (\(W = aL^b\))
  • Beverton-Holt stock-recruitment relationship, with steepness (h) 0.84
  • ageing error
  • two surveys with sex-specific logistic selectivity
  • three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

  • survey indices
  • survey proportions-at-age
  • fishery proportions-at-age

Parameters estimated include:

  • B0
  • parameters for the natural mortality-at-age ogive
  • catchability (q) for the two surveys
  • parameters for the sex-specific selectivity curves for the two surveys
  • parameters for the sex-specific selectivity curves for the three fisheries
  • YCS (recruitment deviations)

1.2 R environment

## [1] "Tue Sep 14 11:23:56 2021"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 11 (bullseye)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_21.08   casal_2.30     devtools_2.4.2 usethis_2.0.1  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.5 
## [11] tidyr_1.1.3    dplyr_1.0.7   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7         lattice_0.20-41    prettyunits_1.1.1  ps_1.6.0          
##  [5] assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.27      utf8_1.2.2        
##  [9] R6_2.5.1           plyr_1.8.6         evaluate_0.14      pillar_1.6.2      
## [13] rlang_0.4.11       rstudioapi_0.13    data.table_1.14.0  callr_3.7.0       
## [17] jquerylib_0.1.4    rmarkdown_2.10     desc_1.3.0         stringr_1.4.0     
## [21] munsell_0.5.0      compiler_3.6.3     xfun_0.25          pkgconfig_2.0.3   
## [25] pkgbuild_1.2.0     htmltools_0.5.2    tidyselect_1.1.1   tibble_3.1.4      
## [29] reshape_0.8.8      fansi_0.5.0        crayon_1.4.1       withr_2.4.2       
## [33] grid_3.6.3         jsonlite_1.7.2     GGally_2.1.2       gtable_0.3.0      
## [37] lifecycle_1.0.0    DBI_1.1.1          magrittr_2.0.1     scales_1.1.1      
## [41] cli_3.0.1          stringi_1.7.4      cachem_1.0.6       remotes_2.4.0     
## [45] fs_1.5.0           testthat_3.0.4     bslib_0.3.0        ellipsis_0.3.2    
## [49] generics_0.1.0     vctrs_0.3.8        RColorBrewer_1.1-2 tools_3.6.3       
## [53] glue_1.4.2         purrr_0.3.4        processx_3.5.2     pkgload_1.2.2     
## [57] fastmap_1.1.0      yaml_2.2.1         colorspace_2.0-2   sessioninfo_1.1.1 
## [61] memoise_2.0.0      knitr_1.34         sass_0.4.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates
rownamesBase_ModelSensitivity_1Percent_Diff
q[tan_sum].q         0.091280.091050.252
q[tan_aut].q         0.126200.125900.238
initialization.B0        309000.00000310700.00000-0.550
natural_mortality.ogive_all112.4900012.98000-3.923
natural_mortality.ogive_all20.132700.127803.693
natural_mortality.ogive_all30.381900.44990-17.806
natural_mortality.ogive_all40.350600.35390-0.941
selectivity[surveysum_sel].male1     4.738004.88100-3.018
selectivity[surveysum_sel].male2     1.750001.77200-1.257
selectivity[surveysum_sel].male3     0.610000.601601.377
selectivity[surveysum_sel].female1   5.460005.61300-2.802
selectivity[surveysum_sel].female2   2.206002.21500-0.408
selectivity[surveyaut_sel].male1     5.504005.64400-2.544
selectivity[surveyaut_sel].male2     2.314002.298000.691
selectivity[surveyaut_sel].male3     0.939200.933100.649
selectivity[surveyaut_sel].female1   5.920006.06200-2.399
selectivity[surveyaut_sel].female2   2.778002.738001.440
selectivity[trawl_sel].male1     8.370008.40400-0.406
selectivity[trawl_sel].male2     1.972001.947001.268
selectivity[trawl_sel].male3     61.65000200.00000-224.412
selectivity[trawl_sel].male4     1.041001.021001.921
selectivity[trawl_sel].female1   8.664008.74100-0.889
selectivity[trawl_sel].female2   2.100002.088000.571
selectivity[trawl_sel].female3   43.3100040.380006.765
selectivity[line_home_sel].male1     11.450008.5830025.039
selectivity[line_home_sel].male2     8.590004.5470047.066
selectivity[line_home_sel].male3     0.380100.2691029.203
selectivity[line_home_sel].female1   9.616009.531000.884
selectivity[line_home_sel].female2   3.875003.685004.903
selectivity[line_spawn_sel].male1     18.3000014.0400023.279
selectivity[line_spawn_sel].male2     13.6700010.0100026.774
selectivity[line_spawn_sel].male3     1.868001.1730037.206
selectivity[line_spawn_sel].female1   9.746009.713000.339
selectivity[line_spawn_sel].female2   3.008002.894003.790
recruitment.YCS1      1.000001.000000.000
recruitment.YCS2      1.000001.000000.000
recruitment.YCS3      1.000001.000000.000
recruitment.YCS4      1.000001.000000.000
recruitment.YCS5      0.485000.466203.876
recruitment.YCS6      0.458300.450101.789
recruitment.YCS7      0.568600.564700.686
recruitment.YCS8      0.566700.566700.000
recruitment.YCS9      0.486100.49070-0.946
recruitment.YCS10     0.555000.56720-2.198
recruitment.YCS11     0.563200.57880-2.770
recruitment.YCS12     0.687600.71090-3.389
recruitment.YCS13     0.620300.63610-2.547
recruitment.YCS14     0.790600.80840-2.251
recruitment.YCS15     0.464300.46930-1.077
recruitment.YCS16     0.700800.70730-0.928
recruitment.YCS17     0.410100.41050-0.098
recruitment.YCS18     0.515000.514500.097
recruitment.YCS19     0.341600.34220-0.176
recruitment.YCS20     0.348300.347300.287
recruitment.YCS21     0.436100.43820-0.482
recruitment.YCS22     0.480600.475001.165
recruitment.YCS23     0.452200.451300.199
recruitment.YCS24     0.491700.49480-0.630
recruitment.YCS25     0.469100.47070-0.341
recruitment.YCS26     0.799300.80490-0.701
recruitment.YCS27     0.790100.79210-0.253
recruitment.YCS28     0.826100.83110-0.605
recruitment.YCS29     0.707600.71250-0.692
recruitment.YCS30     0.551700.55430-0.471
recruitment.YCS31     0.475200.47680-0.337
recruitment.YCS32     0.461700.461400.065
recruitment.YCS33     0.555000.554300.126
recruitment.YCS34     0.546700.542100.841
recruitment.YCS35     0.483200.482500.145
recruitment.YCS36     0.550200.549900.055
recruitment.YCS37     0.615300.61580-0.081
recruitment.YCS38     0.775700.774700.129
recruitment.YCS39     0.631100.630600.079
recruitment.YCS40     0.775500.773500.258
recruitment.YCS41     0.642900.639300.560
recruitment.YCS42     0.706700.699401.033
recruitment.YCS43     0.654300.648600.871
recruitment.YCS44     0.510000.506200.745
recruitment.YCS45     0.586200.58730-0.188
recruitment.YCS46     0.603500.589302.353
recruitment.YCS47     0.576800.574500.399
Casal2 parameter estimates
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              308529.00000308529.00000310577.00000266100.00000266100.00000292654.00000
catchability[summerTANq].q               0.091370.091370.091060.106500.106500.09747
catchability[autumnTANq].q               0.126070.126070.125940.147120.147120.13444
selectivity[M_all].x0              12.4965012.4965012.9844014.4407014.4407013.00000
selectivity[M_all].y0              0.132620.132620.127970.129920.129920.12855
selectivity[M_all].y1              0.382800.382800.447260.288610.288610.35795
selectivity[M_all].y2              0.351130.351130.353730.395600.395600.36956
selectivity[summerTANSel_m].a50             4.739884.739884.876454.577324.577324.69873
selectivity[summerTANSel_m].ato95           1.744591.744591.770291.737641.737641.74362
selectivity[summerTANSel_m].alpha           0.609950.609950.601840.618140.618140.61059
selectivity[summerTANSel_f].a50             5.461115.461115.608075.287985.287985.42487
selectivity[summerTANSel_f].ato95           2.203402.203402.214202.190282.190282.21398
selectivity[autumnTANSel_m].a50             5.509825.509825.639725.730595.730595.49015
selectivity[autumnTANSel_m].ato95           2.312712.312712.297812.990082.990082.34468
selectivity[autumnTANSel_m].alpha           0.941730.941730.933200.960240.960240.93567
selectivity[autumnTANSel_f].a50             5.915745.915746.058485.923445.923445.91564
selectivity[autumnTANSel_f].ato95           2.770202.770202.738463.025293.025292.83473
selectivity[trwlFSel_m].mu              8.369198.369198.402398.040588.040588.31968
selectivity[trwlFSel_m].sigma_l         1.970231.970231.947351.830231.830231.96278
selectivity[trwlFSel_m].sigma_r         61.5229061.52290200.00000173.12600173.12600195.82200
selectivity[trwlFSel_m].alpha           1.042761.042761.020851.032541.032541.03107
selectivity[trwlFSel_f].mu              8.658548.658548.739498.448948.448958.64021
selectivity[trwlFSel_f].sigma_l         2.096562.096562.088492.022882.022882.10291
selectivity[trwlFSel_f].sigma_r         43.1639043.1639040.5947074.4498074.44950196.08500
selectivity[lineHomeFSel_m].a50             11.4560011.456008.6083511.1498011.1497010.33100
selectivity[lineHomeFSel_m].ato95           8.599588.599584.591698.604908.604877.36215
selectivity[lineHomeFSel_m].alpha           0.380220.380220.269930.361590.361590.33090
selectivity[lineHomeFSel_f].a50             9.614769.614769.533529.658729.658719.61305
selectivity[lineHomeFSel_f].ato95           3.870143.870143.690643.958713.958713.89494
selectivity[lineSpawnFSel_m].a50             18.2151018.2151014.0467028.7047028.7047029.95770
selectivity[lineSpawnFSel_m].ato95           13.5995013.5995010.0261019.7122019.7122020.36400
selectivity[lineSpawnFSel_m].alpha           1.856341.856341.174494.702454.702454.98330
selectivity[lineSpawnFSel_f].a50             9.738629.738629.714789.731499.731499.82125
selectivity[lineSpawnFSel_f].ato95           2.993872.993872.896702.949002.949003.10917
process[Recruitment].ycs_values{1972}0.483790.483790.466420.960890.960890.47028
process[Recruitment].ycs_values{1973}0.461220.461220.450200.170290.170290.44943
process[Recruitment].ycs_values{1974}0.568370.568370.564541.338421.338430.55135
process[Recruitment].ycs_values{1975}0.566520.566520.566881.061261.061260.56278
process[Recruitment].ycs_values{1976}0.486350.486350.490810.654520.654520.47857
process[Recruitment].ycs_values{1977}0.554130.554130.567171.116131.116130.55411
process[Recruitment].ycs_values{1978}0.563160.563160.578550.879680.879680.56121
process[Recruitment].ycs_values{1979}0.688990.688990.710941.259091.259090.69474
process[Recruitment].ycs_values{1980}0.620930.620930.636190.978260.978260.62242
process[Recruitment].ycs_values{1981}0.792470.792470.808021.399681.399680.79761
process[Recruitment].ycs_values{1982}0.465070.465070.469280.814050.814050.46578
process[Recruitment].ycs_values{1983}0.699670.699670.707061.218891.218890.70914
process[Recruitment].ycs_values{1984}0.409950.409950.410420.678430.678430.41357
process[Recruitment].ycs_values{1985}0.515400.515400.514560.899680.899680.52216
process[Recruitment].ycs_values{1986}0.341310.341310.342120.633790.633790.34658
process[Recruitment].ycs_values{1987}0.347600.347600.347280.638480.638480.35081
process[Recruitment].ycs_values{1988}0.437910.437910.438260.699060.699060.44356
process[Recruitment].ycs_values{1989}0.479240.479240.475000.845290.845290.48296
process[Recruitment].ycs_values{1990}0.451810.451810.451330.830460.830460.45748
process[Recruitment].ycs_values{1991}0.492640.492640.494790.832780.832780.49530
process[Recruitment].ycs_values{1992}0.469180.469180.470700.841900.841900.47280
process[Recruitment].ycs_values{1993}0.797910.797910.804861.371981.371980.79546
process[Recruitment].ycs_values{1994}0.791280.791280.792081.365601.365600.79353
process[Recruitment].ycs_values{1995}0.825380.825380.831091.336361.336360.82230
process[Recruitment].ycs_values{1996}0.707280.707280.712481.177991.177990.70676
process[Recruitment].ycs_values{1997}0.552060.552060.554270.928430.928430.54976
process[Recruitment].ycs_values{1998}0.475080.475080.476830.811000.811000.47576
process[Recruitment].ycs_values{1999}0.461190.461190.461400.812810.812810.45950
process[Recruitment].ycs_values{2000}0.555750.555750.554420.907700.907700.55642
process[Recruitment].ycs_values{2001}0.545460.545460.542060.899980.899980.54587
process[Recruitment].ycs_values{2002}0.483730.483730.482630.833360.833360.48578
process[Recruitment].ycs_values{2003}0.549890.549890.549930.903890.903890.55113
process[Recruitment].ycs_values{2004}0.614180.614180.615781.026651.026650.62023
process[Recruitment].ycs_values{2005}0.777120.777120.774621.265281.265280.78192
process[Recruitment].ycs_values{2006}0.631300.631300.630521.068971.068970.63677
process[Recruitment].ycs_values{2007}0.773770.773770.773451.195411.195410.77965
process[Recruitment].ycs_values{2008}0.642510.642510.639281.035581.035580.64725
process[Recruitment].ycs_values{2009}0.706490.706490.699351.050051.050050.70700
process[Recruitment].ycs_values{2010}0.653120.653120.648710.987320.987320.65008
process[Recruitment].ycs_values{2011}0.511360.511360.506230.918030.918030.51091
process[Recruitment].ycs_values{2012}0.585560.585560.587380.953840.953840.58606
process[Recruitment].ycs_values{2013}0.600640.600640.589120.965220.965220.60398
process[Recruitment].ycs_values{2014}0.576010.576010.574500.966460.966460.57961
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              0.0000.000-0.66413.75213.7525.145
catchability[summerTANq].q               0.0000.0000.344-16.560-16.560-6.675
catchability[autumnTANq].q               0.0000.0000.105-16.694-16.694-6.634
selectivity[M_all].x0              0.0000.000-3.904-15.558-15.558-4.029
selectivity[M_all].y0              0.0000.0003.5102.0412.0413.071
selectivity[M_all].y1              0.0000.000-16.84024.60624.6066.491
selectivity[M_all].y2              0.0000.000-0.741-12.665-12.665-5.249
selectivity[summerTANSel_m].a50             0.0000.000-2.8813.4303.4300.868
selectivity[summerTANSel_m].ato95           0.0000.000-1.4730.3980.3980.056
selectivity[summerTANSel_m].alpha           0.0000.0001.329-1.344-1.344-0.106
selectivity[summerTANSel_f].a50             0.0000.000-2.6913.1703.1700.664
selectivity[summerTANSel_f].ato95           0.0000.000-0.4900.5950.595-0.480
selectivity[autumnTANSel_m].a50             0.0000.000-2.358-4.007-4.0070.357
selectivity[autumnTANSel_m].ato95           0.0000.0000.644-29.289-29.289-1.382
selectivity[autumnTANSel_m].alpha           0.0000.0000.906-1.965-1.9650.644
selectivity[autumnTANSel_f].a50             0.0000.000-2.413-0.130-0.1300.002
selectivity[autumnTANSel_f].ato95           0.0000.0001.146-9.208-9.208-2.329
selectivity[trwlFSel_m].mu              0.0000.000-0.3973.9263.9260.592
selectivity[trwlFSel_m].sigma_l         0.0000.0001.1617.1067.1060.378
selectivity[trwlFSel_m].sigma_r         0.0000.000-225.082-181.401-181.401-218.291
selectivity[trwlFSel_m].alpha           0.0000.0002.1010.9800.9801.121
selectivity[trwlFSel_f].mu              0.0000.000-0.9352.4212.4210.212
selectivity[trwlFSel_f].sigma_l         0.0000.0000.3853.5143.514-0.303
selectivity[trwlFSel_f].sigma_r         0.0000.0005.952-72.482-72.481-354.280
selectivity[lineHomeFSel_m].a50             0.0000.00024.8572.6732.6749.820
selectivity[lineHomeFSel_m].ato95           0.0000.00046.606-0.062-0.06214.389
selectivity[lineHomeFSel_m].alpha           0.0000.00029.0074.9004.90012.971
selectivity[lineHomeFSel_f].a50             0.0000.0000.845-0.457-0.4570.018
selectivity[lineHomeFSel_f].ato95           0.0000.0004.638-2.289-2.289-0.641
selectivity[lineSpawnFSel_m].a50             0.0000.00022.884-57.587-57.587-64.466
selectivity[lineSpawnFSel_m].ato95           0.0000.00026.276-44.948-44.948-49.741
selectivity[lineSpawnFSel_m].alpha           0.0000.00036.731-153.318-153.318-168.448
selectivity[lineSpawnFSel_f].a50             0.0000.0000.2450.0730.073-0.848
selectivity[lineSpawnFSel_f].ato95           0.0000.0003.2461.4991.499-3.851
process[Recruitment].ycs_values{1972}0.0000.0003.589-98.618-98.6182.792
process[Recruitment].ycs_values{1973}0.0000.0002.38963.07863.0782.557
process[Recruitment].ycs_values{1974}0.0000.0000.675-135.483-135.4852.995
process[Recruitment].ycs_values{1975}0.0000.000-0.064-87.331-87.3310.659
process[Recruitment].ycs_values{1976}0.0000.000-0.916-34.578-34.5781.599
process[Recruitment].ycs_values{1977}0.0000.000-2.353-101.420-101.4200.004
process[Recruitment].ycs_values{1978}0.0000.000-2.733-56.206-56.2060.346
process[Recruitment].ycs_values{1979}0.0000.000-3.185-82.743-82.743-0.835
process[Recruitment].ycs_values{1980}0.0000.000-2.457-57.547-57.547-0.239
process[Recruitment].ycs_values{1981}0.0000.000-1.962-76.622-76.622-0.649
process[Recruitment].ycs_values{1982}0.0000.000-0.906-75.037-75.038-0.152
process[Recruitment].ycs_values{1983}0.0000.000-1.056-74.210-74.210-1.353
process[Recruitment].ycs_values{1984}0.0000.000-0.115-65.490-65.490-0.883
process[Recruitment].ycs_values{1985}0.0000.0000.162-74.561-74.561-1.313
process[Recruitment].ycs_values{1986}0.0000.000-0.236-85.692-85.692-1.545
process[Recruitment].ycs_values{1987}0.0000.0000.091-83.683-83.683-0.925
process[Recruitment].ycs_values{1988}0.0000.000-0.079-59.635-59.635-1.290
process[Recruitment].ycs_values{1989}0.0000.0000.884-76.381-76.381-0.775
process[Recruitment].ycs_values{1990}0.0000.0000.106-83.808-83.808-1.256
process[Recruitment].ycs_values{1991}0.0000.000-0.436-69.043-69.043-0.539
process[Recruitment].ycs_values{1992}0.0000.000-0.325-79.442-79.442-0.772
process[Recruitment].ycs_values{1993}0.0000.000-0.871-71.947-71.9470.307
process[Recruitment].ycs_values{1994}0.0000.000-0.102-72.582-72.582-0.285
process[Recruitment].ycs_values{1995}0.0000.000-0.691-61.908-61.9080.373
process[Recruitment].ycs_values{1996}0.0000.000-0.736-66.552-66.5520.074
process[Recruitment].ycs_values{1997}0.0000.000-0.400-68.176-68.1760.416
process[Recruitment].ycs_values{1998}0.0000.000-0.368-70.707-70.708-0.144
process[Recruitment].ycs_values{1999}0.0000.000-0.045-76.243-76.2430.366
process[Recruitment].ycs_values{2000}0.0000.0000.239-63.330-63.330-0.122
process[Recruitment].ycs_values{2001}0.0000.0000.623-64.995-64.995-0.075
process[Recruitment].ycs_values{2002}0.0000.0000.227-72.280-72.280-0.424
process[Recruitment].ycs_values{2003}0.0000.000-0.008-64.376-64.376-0.226
process[Recruitment].ycs_values{2004}0.0000.000-0.260-67.157-67.157-0.985
process[Recruitment].ycs_values{2005}0.0000.0000.321-62.817-62.817-0.618
process[Recruitment].ycs_values{2006}0.0000.0000.123-69.327-69.327-0.865
process[Recruitment].ycs_values{2007}0.0000.0000.042-54.491-54.491-0.760
process[Recruitment].ycs_values{2008}0.0000.0000.503-61.176-61.176-0.738
process[Recruitment].ycs_values{2009}0.0000.0001.010-48.629-48.629-0.072
process[Recruitment].ycs_values{2010}0.0000.0000.674-51.171-51.1710.464
process[Recruitment].ycs_values{2011}0.0000.0001.004-79.526-79.5260.088
process[Recruitment].ycs_values{2012}0.0000.000-0.311-62.893-62.893-0.086
process[Recruitment].ycs_values{2013}0.0000.0001.918-60.698-60.698-0.555
process[Recruitment].ycs_values{2014}0.0000.0000.262-67.785-67.785-0.626

CASAL objective function component values
ComponentBase_ModelSensitivity_1
Tangaroa_bio_autumn-6.829-6.834
Tangaroa_bio_summer-23.880-23.960
Tangaroa_propn_at_age_aut175.700175.800
Tangaroa_propn_at_age_summer835.900835.600
longline_Campbell_home_propn_at_age275.700275.400
longline_Puysegur_spawn_propn_at_age363.300363.300
trawl_observer_propn_at_age682.600682.300
prior_on_q[tan_sum].q-2.364-2.366
prior_on_q[tan_aut].q-2.033-2.037
prior_on_initialization.B012.64012.650
prior_on_natural_mortality.ogive_all0.0000.000
prior_on_selectivity[surveysum_sel].male0.0000.000
prior_on_selectivity[surveysum_sel].female0.0000.000
prior_on_selectivity[surveyaut_sel].male0.0000.000
prior_on_selectivity[surveyaut_sel].female0.0000.000
prior_on_selectivity[trawl_sel].male0.0000.000
prior_on_selectivity[trawl_sel].female0.0000.000
prior_on_selectivity[line_home_sel].male0.0000.000
prior_on_selectivity[line_home_sel].female0.0000.000
prior_on_selectivity[line_spawn_sel].male0.0000.000
prior_on_selectivity[line_spawn_sel].female0.0000.000
prior_on_recruitment.YCS-14.440-14.370
clp10.0000.000
clp20.0000.000
clp30.0000.000
YCS_average_10.9080.904
Total2297.0002296.000
Casal2 objective function component values
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992                 -1.693-1.693-1.679-1.631-1.631-1.678
observation->summerTANbiomass-1993                 -1.353-1.353-1.331-1.221-1.221-1.318
observation->summerTANbiomass-1994                 -0.975-0.975-0.991-1.091-1.091-1.012
observation->summerTANbiomass-2001                 0.4300.4300.3540.2730.2730.411
observation->summerTANbiomass-2002                 -1.778-1.778-1.786-1.787-1.787-1.778
observation->summerTANbiomass-2003                 -1.685-1.685-1.693-1.688-1.688-1.683
observation->summerTANbiomass-2004                 -1.598-1.598-1.586-1.600-1.600-1.604
observation->summerTANbiomass-2005                 -1.657-1.657-1.656-1.658-1.658-1.658
observation->summerTANbiomass-2006                 -1.143-1.143-1.153-1.179-1.179-1.165
observation->summerTANbiomass-2007                 -1.162-1.162-1.180-1.211-1.211-1.182
observation->summerTANbiomass-2008                 -1.568-1.568-1.553-1.513-1.513-1.553
observation->summerTANbiomass-2009                 -1.700-1.700-1.705-1.715-1.715-1.704
observation->summerTANbiomass-2010                 -1.672-1.672-1.678-1.698-1.698-1.675
observation->summerTANbiomass-2012                 -1.554-1.554-1.558-1.596-1.596-1.552
observation->summerTANbiomass-2013                 -1.669-1.669-1.667-1.634-1.634-1.671
observation->summerTANbiomass-2015                 -1.582-1.582-1.570-1.416-1.416-1.591
observation->summerTANbiomass-2017                 -1.526-1.526-1.528-1.517-1.517-1.526
observation->Tangaroa_propn_at_age_summer-1990                 44.21844.21844.39344.20044.20044.252
observation->Tangaroa_propn_at_age_summer-1992                 51.99351.99351.75352.28352.28352.033
observation->Tangaroa_propn_at_age_summer-1993                 50.20050.20050.16850.26550.26550.218
observation->Tangaroa_propn_at_age_summer-1994                 49.74349.74349.78549.78249.78249.708
observation->Tangaroa_propn_at_age_summer-2001                 48.35548.35548.23748.56848.56848.471
observation->Tangaroa_propn_at_age_summer-2002                 47.83047.83047.87948.03848.03847.817
observation->Tangaroa_propn_at_age_summer-2003                 48.44248.44248.62048.41248.41248.392
observation->Tangaroa_propn_at_age_summer-2004                 44.82344.82344.86544.90344.90344.825
observation->Tangaroa_propn_at_age_summer-2005                 43.09743.09743.11743.06043.06043.126
observation->Tangaroa_propn_at_age_summer-2006                 43.89143.89144.05843.94243.94243.859
observation->Tangaroa_propn_at_age_summer-2007                 41.84841.84841.84141.82441.82441.858
observation->Tangaroa_propn_at_age_summer-2008                 45.22545.22545.26745.12745.12745.217
observation->Tangaroa_propn_at_age_summer-2009                 46.84446.84446.80646.99446.99446.806
observation->Tangaroa_propn_at_age_summer-2010                 47.12847.12847.20247.19647.19647.192
observation->Tangaroa_propn_at_age_summer-2012                 44.35344.35344.18344.77244.77244.409
observation->Tangaroa_propn_at_age_summer-2013                 47.25147.25147.02147.41647.41647.262
observation->Tangaroa_propn_at_age_summer-2015                 46.47346.47346.34246.71846.71846.475
observation->Tangaroa_propn_at_age_summer-2017                 44.18244.18244.08244.20444.20444.191
observation->autumnTANbiomass-1992                 -1.558-1.558-1.572-1.570-1.570-1.559
observation->autumnTANbiomass-1993                 -1.741-1.741-1.733-1.726-1.726-1.738
observation->autumnTANbiomass-1996                 -1.779-1.779-1.779-1.778-1.778-1.778
observation->autumnTANbiomass-1998                 -1.750-1.750-1.750-1.750-1.750-1.750
observation->Tangaroa_propn_at_age_autumn-1992                 44.58944.58944.44344.80544.80544.577
observation->Tangaroa_propn_at_age_autumn-1993                 45.48445.48445.44345.68445.68445.494
observation->Tangaroa_propn_at_age_autumn-1996                 42.18442.18442.29542.48342.48342.185
observation->Tangaroa_propn_at_age_autumn-1998                 43.46443.46443.61043.22543.22543.468
observation->trawl_propn_at_age-1992                 36.06736.06735.94436.59436.59436.013
observation->trawl_propn_at_age-1993                 27.51627.51627.47627.57127.57127.512
observation->trawl_propn_at_age-1994                 25.81925.81925.76425.96425.96425.768
observation->trawl_propn_at_age-1996                 28.39428.39428.39728.61728.61728.441
observation->trawl_propn_at_age-1998                 24.91524.91524.91025.03225.03224.920
observation->trawl_propn_at_age-2001                 24.58024.58024.54224.68524.68524.563
observation->trawl_propn_at_age-2002                 26.77026.77026.79226.93626.93626.779
observation->trawl_propn_at_age-2003                 34.56434.56434.51134.57034.57034.586
observation->trawl_propn_at_age-2004                 29.60829.60829.60829.60429.60429.505
observation->trawl_propn_at_age-2005                 30.14730.14730.16630.26730.26730.125
observation->trawl_propn_at_age-2006                 33.62933.62933.71433.72933.72933.593
observation->trawl_propn_at_age-2007                 26.63526.63526.58826.66226.66226.617
observation->trawl_propn_at_age-2008                 27.05927.05927.07627.05327.05327.077
observation->trawl_propn_at_age-2009                 37.21337.21337.23737.21037.21037.217
observation->trawl_propn_at_age-2010                 30.64830.64830.69430.59430.59430.722
observation->trawl_propn_at_age-2011                 31.26631.26631.26031.33931.33931.245
observation->trawl_propn_at_age-2012                 32.32532.32532.36632.23732.23732.363
observation->trawl_propn_at_age-2013                 37.07237.07236.94336.84336.84336.957
observation->trawl_propn_at_age-2014                 30.64030.64030.64230.57630.57630.632
observation->trawl_propn_at_age-2015                 33.45633.45633.47433.32733.32733.491
observation->trawl_propn_at_age-2016                 36.53236.53236.48236.36836.36836.534
observation->trawl_propn_at_age-2017                 37.75537.75537.70837.64137.64137.795
observation->longline_Campbell_home_propn_at_age-1999                 45.34845.34845.25645.14345.14345.309
observation->longline_Campbell_home_propn_at_age-2001                 31.96531.96531.95031.93431.93431.984
observation->longline_Campbell_home_propn_at_age-2003                 28.64428.64428.67528.61028.61028.677
observation->longline_Campbell_home_propn_at_age-2005                 32.75032.75032.77632.82632.82632.749
observation->longline_Campbell_home_propn_at_age-2009                 26.03326.03325.61125.88625.88625.939
observation->longline_Campbell_home_propn_at_age-2010                 24.30224.30224.46124.33824.33824.326
observation->longline_Campbell_home_propn_at_age-2011                 28.87828.87828.93528.74728.74728.882
observation->longline_Campbell_home_propn_at_age-2012                 32.25832.25832.38932.24932.24932.279
observation->longline_Campbell_home_propn_at_age-2014                 25.49525.49525.35725.39125.39125.451
observation->longline_Puyseger_home_propn_at_age-2000                 42.74542.74542.68042.95642.95643.129
observation->longline_Puyseger_home_propn_at_age-2001                 31.77031.77031.90031.79131.79131.977
observation->longline_Puyseger_home_propn_at_age-2002                 39.97839.97839.99840.17940.17940.361
observation->longline_Puyseger_home_propn_at_age-2003                 43.52743.52743.51143.69443.69443.560
observation->longline_Puyseger_home_propn_at_age-2004                 39.95739.95740.01540.07640.07640.140
observation->longline_Puyseger_home_propn_at_age-2005                 25.53225.53225.35825.50625.50625.482
observation->longline_Puyseger_home_propn_at_age-2006                 35.21035.21035.42635.10735.10735.010
observation->longline_Puyseger_home_propn_at_age-2007                 33.98133.98133.78234.13734.13734.361
observation->longline_Puyseger_home_propn_at_age-2008                 19.13919.13919.11319.09019.09019.135
observation->longline_Puyseger_home_propn_at_age-2010                 24.23824.23824.36624.03824.03823.920
observation->longline_Puyseger_home_propn_at_age-2017                 27.20027.20027.09327.44127.44127.656
prior->B0->process[Recruitment].b0              12.64012.64012.64612.49212.49212.587
prior->summerTANq->catchability[summerTANq].q               -2.363-2.363-2.365-2.240-2.240-2.318
prior->autumnTANq->catchability[autumnTANq].q               -2.035-2.035-2.037-1.786-1.786-1.939
prior->M_all_x0->selectivity[M_all].x0              0.0000.0000.0000.0000.0000.000
prior->M_all_y0->selectivity[M_all].y0              0.0000.0000.0000.0000.0000.000
prior->M_all_y1->selectivity[M_all].y1              0.0000.0000.0000.0000.0000.000
prior->M_all_y2->selectivity[M_all].y2              0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].mu              0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].sigma_l         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].sigma_r         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].mu              0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].sigma_l         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].sigma_r         0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->process[Recruitment].ycs_values{1972}-0.378-0.378-0.365-0.008-0.008-0.368
prior->process[Recruitment].ycs_values{1973}-0.360-0.360-0.3491.3241.324-0.348
prior->process[Recruitment].ycs_values{1974}-0.397-0.397-0.3980.5940.594-0.399
prior->process[Recruitment].ycs_values{1975}-0.398-0.398-0.3980.1430.143-0.398
prior->process[Recruitment].ycs_values{1976}-0.380-0.380-0.383-0.361-0.361-0.375
prior->process[Recruitment].ycs_values{1977}-0.399-0.399-0.3980.2300.230-0.399
prior->process[Recruitment].ycs_values{1978}-0.398-0.398-0.396-0.122-0.122-0.398
prior->process[Recruitment].ycs_values{1979}-0.335-0.335-0.3160.4620.462-0.330
prior->process[Recruitment].ycs_values{1980}-0.380-0.380-0.3720.0170.017-0.379
prior->process[Recruitment].ycs_values{1981}-0.231-0.231-0.2130.6960.696-0.225
prior->process[Recruitment].ycs_values{1982}-0.364-0.364-0.367-0.206-0.206-0.364
prior->process[Recruitment].ycs_values{1983}-0.326-0.326-0.3190.3960.396-0.318
prior->process[Recruitment].ycs_values{1984}-0.291-0.291-0.292-0.343-0.343-0.297
prior->process[Recruitment].ycs_values{1985}-0.394-0.394-0.393-0.095-0.095-0.395
prior->process[Recruitment].ycs_values{1986}-0.114-0.114-0.117-0.373-0.373-0.132
prior->process[Recruitment].ycs_values{1987}-0.135-0.135-0.134-0.371-0.371-0.146
prior->process[Recruitment].ycs_values{1988}-0.334-0.334-0.334-0.326-0.326-0.341
prior->process[Recruitment].ycs_values{1989}-0.375-0.375-0.372-0.167-0.167-0.378
prior->process[Recruitment].ycs_values{1990}-0.350-0.350-0.350-0.186-0.186-0.356
prior->process[Recruitment].ycs_values{1991}-0.384-0.384-0.385-0.183-0.183-0.385
prior->process[Recruitment].ycs_values{1992}-0.367-0.367-0.369-0.171-0.171-0.370
prior->process[Recruitment].ycs_values{1993}-0.225-0.225-0.2170.6500.650-0.228
prior->process[Recruitment].ycs_values{1994}-0.233-0.233-0.2320.6390.639-0.230
prior->process[Recruitment].ycs_values{1995}-0.192-0.192-0.1850.5900.590-0.196
prior->process[Recruitment].ycs_values{1996}-0.319-0.319-0.3150.3290.329-0.320
prior->process[Recruitment].ycs_values{1997}-0.399-0.399-0.399-0.055-0.055-0.399
prior->process[Recruitment].ycs_values{1998}-0.372-0.372-0.373-0.209-0.209-0.373
prior->process[Recruitment].ycs_values{1999}-0.360-0.360-0.360-0.207-0.207-0.358
prior->process[Recruitment].ycs_values{2000}-0.399-0.399-0.399-0.084-0.084-0.399
prior->process[Recruitment].ycs_values{2001}-0.399-0.399-0.399-0.094-0.094-0.399
prior->process[Recruitment].ycs_values{2002}-0.378-0.378-0.377-0.182-0.182-0.380
prior->process[Recruitment].ycs_values{2003}-0.399-0.399-0.399-0.089-0.089-0.399
prior->process[Recruitment].ycs_values{2004}-0.383-0.383-0.3830.0900.090-0.381
prior->process[Recruitment].ycs_values{2005}-0.249-0.249-0.2510.4720.472-0.243
prior->process[Recruitment].ycs_values{2006}-0.375-0.375-0.3750.1550.155-0.372
prior->process[Recruitment].ycs_values{2007}-0.252-0.252-0.2530.3580.358-0.246
prior->process[Recruitment].ycs_values{2008}-0.368-0.368-0.3700.1040.104-0.365
prior->process[Recruitment].ycs_values{2009}-0.320-0.320-0.3260.1260.126-0.320
prior->process[Recruitment].ycs_values{2010}-0.362-0.362-0.3640.0310.031-0.364
prior->process[Recruitment].ycs_values{2011}-0.392-0.392-0.390-0.069-0.069-0.392
prior->process[Recruitment].ycs_values{2012}-0.394-0.394-0.393-0.018-0.018-0.394
prior->process[Recruitment].ycs_values{2013}-0.389-0.389-0.393-0.002-0.002-0.388
prior->process[Recruitment].ycs_values{2014}-0.396-0.396-0.3960.0000.000-0.395
additional_prior->YCS_average_1                 0.9080.9080.9040.0060.0060.905
total_negloglike                 2296.9702296.9702296.1402317.7102317.7102298.450
total_score                 2296.9702296.9702296.1402317.7102317.7102298.450

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"                                                                  
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## [1] "[IMPORTANT] FMM: Small step size convergence"
## [2] "FMM: Small step size convergence"
## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] ""

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"